After the 2006 federal election Goodyear was elected Standing committee chair of the Procedure and House Affairs Committee (of which he chairs the Subcommittee on Parliament Hill Security.) In March 2008 the Procedure and House Affairs Committee ousted Goodyear by moving a motion of non-confidence in him. The committee then elected Conservative MP Joe Preston as the chair against his will, and he called no meetings before resigning from his position. The committee currently has no chair and has not met since March 6. Jay Hill, Conservative party whip, said he is adamant that unless the opposition is willing to meet to re-elect Goodyear as the chair and to withdraw the motion to study the In and Out scandal, there will be no Procedure and House Affairs committee meetings.[5] The Speaker of the House made a ruling on the events in this committee and others which stated rulings by committee chairs are being routinely overturned by majority votes, even when the rulings are procedurally sound. Such a state of affairs has led to "general lawlessness" at committees.[6] Goodyear also chairs Subcommittee on Agenda and Procedure He was also named Chairman of the all-party Canada-Armenia Parliamentary Friendship Group.

A former campaign manager for Goodyear admits he negotiated a lease for a campaign headquarters in 2004 that said the landlord would make a political donation to Goodyear's election bid. In a compliance agreement with the Commissioner of Canada Elections, Reg Petersen "acknowledged an act that constitutes an offence" under the Elections Act.[7] The Conservative Party’s spokesperson, Ryan Sparrow, responded that the error was a mistake made by a first-time campaign manager and noted that “Elections Canada has acknowledged that [Peterson] made a mistake and no further action has been taken.” [8]

In 2009 named Minister of State responsible for the Federal Economic Development Agency for Southern Ontario (FedDev Ontario) created by the federal government through Budget 2009 to "support Ontario’s then floundering economy."[9] FedDev Ontario had a $1-billion budget for 2009-2014.[9] Among other things, FedDev helped small companies develop new products faster,[citation needed] similar to the role played by the Industrial Research Assistance Program (NRC IRAP).

In May 2012 Jameson Berkow of reported in the Financial Post that halfway its mandate, "Mr. Goodyear’s Federal Economic Development Agency for Southern Ontario [...] appears to have enjoyed unbridled success in helping Canada’s most populous province save itself from economic oblivion.”[9]

Under the federal Minister of State for Science and Technology, Gary Goodyear, the NRC became a "toolbox for industry" and dented basic-research infrastructure.[10]

Goodyear, the minister of state for science and technology, has presided over the most retrograde federal Science and Technology policy in memory. During his tenure, the government shuttered the office of the National Science Adviser, blocked asbestos from a UN hazardous chemicals list on which it clearly belongs, gutted the Fisheries Act, gutted the Navigable Waters Protection Act, set out to weaken the Species at Risk Act, killed the long-form census, eroded Environment Canada’s ability to monitor climate change, earned an international reputation for muzzling scientists and, at a great potential cost, defunded the world’s leading freshwater research centre... At the same time, changes to our science-funding regime and a makeover of the National Research Council, Canada’s science agency, into a tool box for industry have dented our basic-research infrastructure and damaged our prospects for innovation.

— Himelfarb 2014

In early 2009, Goodyear oversaw $147.9 million in funding cuts [11] for science programs, the most prominent being the lack of any funding for new projects for Genome Canada.[12] Critics of the cuts, including a team of neuroscientists who lost funding, argued that when coupled with the Obama administration's increased funding for science, the cuts could produce a brain drain as researchers move to the United States and secure funding.[13]

June 2009 saw Goodyear recommending the SSHRC withdraw a $19,750 funding grant for a future of Israel and Palestine conference[14] because it was deemed by the Minister to be too anti-Israel.[15] Goodyear responded, saying that he did call the SSHRC to ask for a funding review, but denied he asked them to cancel the grant.[16]

Under Goodyear, federal science and technology expenditures reached nearly $11.9 billion in 2010–11.[17] In the Economic Action Plan 2012, the federal government announced that one billion new dollars are to be invested in science and technology.[18]

Under the Economic Action Plan, the National Research Council was transformed into a research and technology organization that focuses on "business-led research."[19] On 7 May 2013, the NRC launched its new "business approach" in which it offered only four "business lines": "strategic research and development, technical services, management of science and technology infrastructure and NRC-Industrial Research Assistance Program (IRAP). These four business lines are intended to shorten the gap between early stage research and development and commercialization.[19] NRC is focus "real-world applications"[20] was the creation of the Canadian Wheat Alliance, (CWA) in 2013 [21] with NRC, Agriculture and Agri-Food Canada, the Government of Saskatchewan and the University of Saskatchewan.[20] With a budget of approximately $97 million (2013-2018), the Canadian Wheat Alliance will study improving the yield of Canadian wheat even in extreme weather, integrating "basic research with genetic improvement"[22] of wheat crops, and research on efficient use of chemical fertilizers.[20] Working with the Crop Development Centre they will be integrating "basic research with genetic improvement"[22] of wheat. The second major industry-led research in 2013 is the Algal Carbon Conversion Pilot Project, [21] development of an algae system to recycle carbon emissions from the oil sands, with plans for a $19 million facility to be constructed in Alberta, in partnership between the NRC and industry partners, Canadian Natural Resources Limited (Canadian Natural) and Pond Biofuels.[21]

The Canadian Wheat Alliance will improve the quality of Canadian wheat, and enhance Canada’s competitive position in the growing world market," said Federal Agriculture Minister Gerry Ritz, on behalf of the Honorable Gary Goodyear, Minister of State (Science and Technology). "The benefits of this Alliance will flow throughout the entire value chain, strengthening our producers’ bottom lines and our overall economy.

In a March 2009 interview, The Globe and Mail asked Goodyear if he believed in evolution. He responded, "I am a Christian, and I don't think anybody asking a question about my religion is appropriate." While many scientists and educators expressed shock at this,[25] others defended the minister, citing statistics that show a majority of Canadians believe God played a role in creation.[26] Later that day, however, Goodyear said that he believed in evolution during an interview with CTV News.[27] When asked to clarify this belief, Goodyear responded "We are evolving, every year, every decade. That’s a fact. Whether it’s to the intensity of the sun, whether it’s to, as a chiropractor, walking on cement versus anything else, whether it’s running shoes or high heels, of course, we are evolving to our environment."[28] He also garnered criticism from MP Elizabeth May, among others, for a comment during a debate on an NDP opposition motion in June 2012. Parliamentary proceedings for June 5, 2012, record Goodyear as saying,[29]

Madam Speaker, what I would recommend to the hon. member is that when he tightens that towel around his neck at nighttime that he not do it for more than 20 seconds. It actually ends up causing cerebral anoxia that leaves permanent brain damage.

— Goodyear 5 June 2012

This comment was in response to a question by MP Bruce Hyer, again concerning Goodyear's belief in evolution,[29]

I have a broad question for the minister. Does he really believe in science and the implications of scientific inquiry? I have a more specific question that will put a fine point on it. There is a vast bunch of science out there that says that life was created on this planet three to four billion years ago, and there are other theories. Does the minister believe that life was created on this planet through evolution three to four billion years ago or does he subscribe to a different theory?

Goodyear and his wife Valerie are co-owners of Constant Energy Inc. Constant Energy is a creditor in the bankruptcy of Imagine Adoption.[30] Constant Energy’s total outstanding claim at $96,000 is the first entry on the list of preferred creditors for wages/rent/etc. TheStar also reported on the issue.[31] Valerie was also an employee of Imagine Adoption.[32] In April 2011 the agency’s founder and its general manager were charged with breach of trust and multiple counts of fraud.[33] As of April 2012 the case has not yet gone before the courts.[34]